Align gluconokinase (EC 2.7.1.12) (characterized)
to candidate PP_3416 PP_3416 D-gluconate kinase
Query= BRENDA::Q8NMT0 (167 letters) >FitnessBrowser__Putida:PP_3416 Length = 179 Score = 133 bits (335), Expect = 1e-36 Identities = 76/164 (46%), Positives = 97/164 (59%), Gaps = 8/164 (4%) Query: 9 IVVMGVSGCGKSSVGKALAAELGIEYKDGDELHPQENIDKMASGQALDDDDRAWWLVQVG 68 IVVMGV+GCGKS +G A+AA G +GD HP ENI KM++G LDD DRA WLV++G Sbjct: 8 IVVMGVAGCGKSCIGAAIAARSGGRLIEGDAFHPAENIRKMSAGIPLDDSDRAGWLVRLG 67 Query: 69 KWLR------DRPSGVIACSALKRSYRDLLRTKCPGTVFVHLHGDYDLLLSRMKAREDHF 122 + L+ +RP ++ CSALKR YRD LR PG VFV L R+ AR HF Sbjct: 68 EELQATTQAGERP--ILTCSALKRRYRDTLRDAMPGLVFVFLELSPAEAEKRVLARPGHF 125 Query: 123 MPSTLLDSQFATLEPLEDDEDGKVFDVAHTISELAAQSAEWVRN 166 MP++L+DSQFA LE + D I LA W+++ Sbjct: 126 MPASLIDSQFAALESPRGEPLTLALDATQPIEALAEAVDHWLKH 169 Lambda K H 0.318 0.134 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 86 Number of extensions: 4 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 167 Length of database: 179 Length adjustment: 18 Effective length of query: 149 Effective length of database: 161 Effective search space: 23989 Effective search space used: 23989 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory